Journal article

Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana

Mary M Rorick, Edward B Baskerville, Thomas S Rask, Karen P Day, Mercedes Pascual

PLOS COMPUTATIONAL BIOLOGY | PUBLIC LIBRARY SCIENCE | Published : 2018

Abstract

A challenge in studying diverse multi-copy gene families is deciphering distinct functional types within immense sequence variation. Functional changes can in some cases be tracked through the evolutionary history of a gene family; however phylogenetic approaches are not possible in cases where gene families diversify primarily by recombination. We take a network theoretical approach to functionally classify the highly recombining var antigenic gene family of the malaria parasite Plasmodium falciparum. We sample var DBLα sequence types from a local population in Ghana, and classify 9,276 of these variants into just 48 functional types. Our approach is to first decompose each sequence type in..

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University of Melbourne Researchers

Grants

Awarded by Fogarty International Center at National Institutes of Health Program on the Ecology and Evolution of Infectious Diseases (EEID)


Awarded by National Institute of Allergy and Infectious Disease, National Institutes of Health


Awarded by FOGARTY INTERNATIONAL CENTER


Awarded by NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES


Funding Acknowledgements

This work was funded by: Fogarty International Center at National Institutes of Health Program on the Ecology and Evolution of Infectious Diseases (EEID) [Grant number: R01-TW009670]; and the National Institute of Allergy and Infectious Disease, National Institutes of Health [Grant number: R01-A1084156]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.